DockIntoDensityUtils.hh File Reference

Utils for folding into density. More...

#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <protocols/electron_density/DensitySymmInfo.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <queue>

Classes
class	protocols::electron_density::RBfitResult
	CLASSES. More...
class	protocols::electron_density::RefinementResult
class	protocols::electron_density::RBfitResultComparitor
class	protocols::electron_density::RefinementResultComparitor
class	protocols::electron_density::RevRefinementResultComparitor
class	protocols::electron_density::PointScoreComparator
class	protocols::electron_density::ResultDB< T, Tcomp >
struct	protocols::electron_density::PoseSphericalSamplesOptions
struct	protocols::electron_density::SelectDensityPointsOptions
struct	protocols::electron_density::DensityGridSearchOptions

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::electron_density

Typedefs
typedef ResultDB< RBfitResult, RBfitResultComparitor >	protocols::electron_density::RBfitResultDB
typedef ResultDB< RefinementResult, RefinementResultComparitor >	protocols::electron_density::RefinementResultDB
typedef ResultDB< RefinementResult, RevRefinementResultComparitor >	protocols::electron_density::RevRefinementResultDB

Functions
template<typename T >
void	protocols::electron_density::write_RBfitResultDB (RBfitResultDB fit_result_DB, T &outresults)
	FUNCTIONS. More...
template<typename T >
void	protocols::electron_density::dump_RefinementDB_to_silent (T resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)
void	protocols::electron_density::compare_RBfitDB_to_native (RBfitResultDB resultDB, core::pose::Pose const &pose, core::pose::PoseCOPs const &natives, utility::vector1< numeric::xyzVector< core::Real > > const &native_coms, utility::vector1< numeric::xyzVector< core::Real > > const &native_middle_cas, DensitySymmInfo const &symminfo, bool const rot_middle_ca, core::Real const rms_cutoff)
core::Real	protocols::electron_density::get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d)
core::Real	protocols::electron_density::get_rms (RefinementResult const &r1, RefinementResult const &r2, DensitySymmInfo const &d)
core::Real	protocols::electron_density::get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool const native)
core::Real	protocols::electron_density::get_gdt (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool native)
void	protocols::electron_density::apply_transform (core::pose::Pose &pose, RBfitResult const &transform)
	FUNCTIONS. More...
core::Real	protocols::electron_density::get_rot_angle (numeric::xyzMatrix< core::Real > const &R)
void	protocols::electron_density::pose_spherical_samples (core::pose::Pose const &pose, ObjexxFCL::FArray3D< core::Real > &sigR, ObjexxFCL::FArray3D< core::Real > &epsR, PoseSphericalSamplesOptions const &params)
	Step 0: map pose to spherically sampled density + mask. More...
core::Real	protocols::electron_density::get_radius (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &com, bool const center_on_middle_ca)
	Get max extent of pose. More...
void	protocols::electron_density::map_from_spectrum (utility::vector1< core::Real > const &pose_1dspec, ObjexxFCL::FArray3D< core::Real > &rot, core::Real const delR)
void	protocols::electron_density::dump_points_to_search_to_pdb_or_txt (utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, std::string const &pdb_filename, std::string const &txt_filename)
utility::vector1< numeric::xyzVector< core::Real > >	protocols::electron_density::select_density_points (core::pose::Pose const &pose, SelectDensityPointsOptions const &params, core::Size &nRsteps)
core::Real	protocols::electron_density::get_spectrum (core::pose::Pose const &pose, utility::vector1< core::Real > &pose_1dspec, core::Real const delR, core::Real const fragDens, bool const convolute_single_residue, bool const center_on_middle_ca)
	Get 1d power spectrum of a pose. More...
void	protocols::electron_density::cluster_RefinementDB (RefinementResultDB &results, DensitySymmInfo const &symminfo, core::Real const cluster_radius, core::Size const target_size=0)
	cluster a RefinementResultDB based on a specific cluster_radius. If target_size is unset or More...
void	protocols::electron_density::do_filter (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results, bool const rescore, DensitySymmInfo const &symminfo, core::Real const cluster_radius)
void	protocols::electron_density::cluster_RBfitResultDB_fast (RBfitResultDB &results, core::Size const delR, core::Size const nRsteps, core::Real const cluster_radius, core::Size const max_results, bool const include_distance, core::scoring::electron_density::ElectronDensity const &dens)
void	protocols::electron_density::density_grid_search (core::Size pose_idx, core::pose::Pose const &pose, RBfitResultDB &results, utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, DensityGridSearchOptions const &params)
	do the main search over the map More...

Detailed Description

Utils for folding into density.

Author

Frank DiMaio

Danny Farrell